The problem is that Style.Include pushes a style link into the header, in other words it doesn't render in place - but your conditional comments do. So if you look at the HTML source of your page output, you'll see there's just an empty conditional tag.

I saw a comment somewhere from one of the Orchard devs about properly supporting conditionals in the future.

Until then you'll just have to override Document.cshtml and place the conditional and style link manually in the header yourself.